YCKC - BACSU - GREMLIN Contacts

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YCKC - Uncharacterized protein YckC

UniProt:	P42401	Sequences: MNIYKPAGFWIRLGAALLDYIIVSVPLLLIYWLITGKDPNDSMFISLVVLLYSILLPMFWRGYLIGKRICGIRIVKKDGSQVSLLTMFLRVIVAGLVYCITFGLGLIASLILIAVREDKRTLHDLIAGTYVTYATPGEEELNADEEIRKSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	151 (124)
Sequences:	2760 (2214)
Seq/√Len:	198.8

BACSU - YCKC YCZC YTEJ YXAI

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_L	65_I	3.805	1.00
11_I	133_Y	3.596	1.00
120_R	125_L	3.469	1.00
116_R	125_L	3.283	1.00
76_K	86_T	2.926	1.00
113_I	121_T	2.759	1.00
82_V	87_M	2.676	1.00
18_L	70_C	2.617	1.00
7_A	72_I	2.457	1.00
55_L	59_F	2.390	1.00
75_V	132_T	2.277	1.00
82_V	129_T	2.252	1.00
112_L	122_L	2.243	1.00
63_Y	68_R	2.199	1.00
94_A	126_I	2.052	1.00
14_G	70_C	1.995	1.00
112_L	116_R	1.945	1.00
77_K	120_R	1.787	1.00
58_M	84_L	1.766	1.00
32_W	36_G	1.721	1.00
116_R	120_R	1.625	1.00
118_D	130_Y	1.562	1.00
75_V	130_Y	1.493	1.00
56_L	60_W	1.467	1.00
73_R	134_A	1.454	1.00
83_S	86_T	1.450	1.00
76_K	80_S	1.443	1.00
50_L	88_F	1.401	1.00
98_Y	123_H	1.386	1.00
104_L	107_I	1.376	1.00
5_K	133_Y	1.333	1.00
89_L	93_V	1.317	1.00
18_L	69_I	1.300	1.00
61_R	68_R	1.265	1.00
53_S	57_P	1.255	1.00
24_S	28_L	1.254	1.00
71_G	135_T	1.247	1.00
89_L	126_I	1.219	1.00
52_Y	57_P	1.209	1.00
76_K	83_S	1.205	1.00
63_Y	134_A	1.202	1.00
98_Y	106_L	1.193	1.00
21_I	25_V	1.191	1.00
6_P	9_F	1.191	1.00
15_A	72_I	1.179	1.00
85_L	89_L	1.178	1.00
11_I	70_C	1.145	1.00
56_L	68_R	1.143	1.00
77_K	130_Y	1.138	1.00
9_F	113_I	1.134	1.00
9_F	114_A	1.133	1.00
16_A	53_S	1.120	1.00
57_P	74_I	1.094	1.00
58_M	87_M	1.082	1.00
8_G	11_I	1.048	1.00
120_R	130_Y	1.047	1.00
95_G	98_Y	1.046	1.00
26_P	48_V	1.046	1.00
77_K	128_G	1.012	1.00
6_P	130_Y	1.008	1.00
57_P	67_K	1.006	1.00
101_T	122_L	1.002	1.00
57_P	121_T	0.992	1.00
98_Y	101_T	0.975	0.99
92_I	95_G	0.954	0.99
17_L	21_I	0.938	0.99
53_S	64_L	0.934	0.99
15_A	67_K	0.931	0.99
93_V	102_F	0.924	0.99
62_G	73_R	0.923	0.99
38_D	41_D	0.901	0.99
98_Y	121_T	0.883	0.99
105_G	122_L	0.862	0.99
59_F	62_G	0.854	0.99
19_D	66_G	0.851	0.99
65_I	69_I	0.850	0.99
18_L	22_I	0.846	0.99
51_L	55_L	0.840	0.98
11_I	14_G	0.835	0.98
54_I	87_M	0.834	0.98
54_I	88_F	0.832	0.98
16_A	20_Y	0.822	0.98
74_I	87_M	0.808	0.98
124_D	127_A	0.804	0.98
97_V	101_T	0.803	0.98
13_L	113_I	0.802	0.98
6_P	119_K	0.795	0.98
33_L	36_G	0.790	0.98
72_I	131_V	0.774	0.97
99_C	106_L	0.771	0.97
88_F	93_V	0.768	0.97
50_L	54_I	0.766	0.97
76_K	128_G	0.766	0.97
112_L	115_V	0.752	0.97
52_Y	58_M	0.750	0.97
54_I	92_I	0.748	0.97
35_T	41_D	0.746	0.97
8_G	113_I	0.738	0.97
76_K	82_V	0.730	0.96
49_V	53_S	0.727	0.96
26_P	29_L	0.727	0.96
118_D	125_L	0.720	0.96
104_L	112_L	0.720	0.96
101_T	105_G	0.716	0.96
31_Y	35_T	0.711	0.96
60_W	63_Y	0.706	0.96
57_P	92_I	0.705	0.96
10_W	14_G	0.696	0.95
94_A	127_A	0.695	0.95
54_I	58_M	0.695	0.95
19_D	64_L	0.695	0.95
60_W	65_I	0.693	0.95
63_Y	87_M	0.692	0.95
90_R	124_D	0.687	0.95
94_A	98_Y	0.686	0.95
8_G	114_A	0.684	0.95
76_K	129_T	0.682	0.95
7_A	133_Y	0.671	0.94
84_L	88_F	0.669	0.94
67_K	131_V	0.667	0.94
86_T	89_L	0.665	0.94
21_I	24_S	0.665	0.94
67_K	74_I	0.663	0.94
43_M	47_L	0.663	0.94
102_F	105_G	0.657	0.94
22_I	26_P	0.655	0.93
57_P	123_H	0.654	0.93
58_M	83_S	0.654	0.93
62_G	75_V	0.649	0.93
20_Y	34_I	0.647	0.93
57_P	95_G	0.642	0.93
98_Y	105_G	0.639	0.93
84_L	87_M	0.638	0.93
57_P	128_G	0.636	0.92
112_L	125_L	0.633	0.92
93_V	98_Y	0.629	0.92
130_Y	133_Y	0.628	0.92
102_F	113_I	0.625	0.92
8_G	119_K	0.618	0.91
10_W	17_L	0.615	0.91
22_I	69_I	0.614	0.91
59_F	84_L	0.612	0.91
87_M	92_I	0.612	0.91
82_V	96_L	0.606	0.91
112_L	117_E	0.605	0.90
113_I	119_K	0.603	0.90
51_L	84_L	0.601	0.90
97_V	100_I	0.600	0.90
59_F	81_Q	0.596	0.90
37_K	45_I	0.594	0.90
51_L	54_I	0.589	0.89
92_I	105_G	0.588	0.89
107_I	114_A	0.586	0.89
27_L	49_V	0.585	0.89
7_A	131_V	0.583	0.89
103_G	106_L	0.583	0.89
29_L	33_L	0.581	0.89
101_T	104_L	0.580	0.89
48_V	51_L	0.579	0.88
11_I	72_I	0.578	0.88
7_A	11_I	0.572	0.88
22_I	25_V	0.571	0.88
27_L	45_I	0.568	0.87
24_S	36_G	0.565	0.87
95_G	123_H	0.565	0.87
85_L	126_I	0.562	0.87
56_L	63_Y	0.561	0.87
60_W	68_R	0.552	0.86
13_L	17_L	0.545	0.85
13_L	16_A	0.541	0.85
55_L	60_W	0.537	0.84
9_F	13_L	0.533	0.84
11_I	71_G	0.531	0.84
68_R	134_A	0.529	0.84
96_L	101_T	0.529	0.84
63_Y	72_I	0.528	0.83
35_T	38_D	0.526	0.83
75_V	81_Q	0.524	0.83
74_I	131_V	0.521	0.83
30_I	42_S	0.516	0.82
94_A	123_H	0.510	0.81
112_L	118_D	0.509	0.81
62_G	81_Q	0.505	0.81
113_I	131_V	0.503	0.80
21_I	69_I	0.501	0.80
107_I	115_V	0.500	0.80

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4tr3A	1	0.6556	13.1	0.932	Contact Map
2cvbA	1	0.5762	8.9	0.937	Contact Map
3kijA	1	0.5629	7.8	0.939	Contact Map
2p5qA	3	0.5232	7.2	0.94	Contact Map
4hdeA	1	0.5894	6.1	0.942	Contact Map
1xzoA	3	0.596	5.5	0.943	Contact Map
3hczA	2	0.5695	5	0.944	Contact Map
3j8eG	3	0.8675	4.9	0.944	Contact Map
2v1mA	1	0.5364	4.8	0.944	Contact Map
2lrnA	1	0.5629	4.1	0.946	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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